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The only thing we can think it might be is we were doing 301 redirects to change the file names, but why would it leave out the www?
301 redirects appear to be causing havoc with google for us, we are getting more pages going in on a daily basis but now we have noticed our index page disappear.
The important thing is, that these are showing up where there are ONLY absolute links done one way, with the www, and ONLY links that the webmaster knows about, which are also absolute links, with the www. Even brand new domains that no one whatsoever is linking to, except maybe the web designer - with one link, absolute with the www.
They are URL only, which means that the content isn't indexed with it, and are without a shadow of a doubt coming from someplace else - from a link someplace else that is beyond the webmaster's knowledge or control.
I believe that Google is getting the URLs, wirhout the www, from a database of whois records that has access to the info as soon as a registered site is put on hosting.
I'm talking about the root domain.